bio::liveseq::range(3pm) [debian man page]
Bio::LiveSeq::Range(3pm) User Contributed Perl Documentation Bio::LiveSeq::Range(3pm) NAME
Bio::LiveSeq::Range - Range abstract class for LiveSeq SYNOPSIS
# documentation needed DESCRIPTION
This is used as parent for exon and intron classes. AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $range1 = Bio::LiveSeq::Range->new(-seq => $obj_ref, -start => $beginlabel, -end => $endlabel, -strand => 1); Function: generates a new Bio::LiveSeq::Range Returns : reference to a new object of class Range Errorcode -1 Args : two labels, an obj_ref and an integer strand 1=forward strand, strand -1=reverse strand if strand not specified, it defaults to 1 the -seq argument must point to the underlying DNA LiveSeq object valid Title : valid Usage : $boolean = $obj->valid($label) Function: tests if a label exists AND is part of the object Returns : boolean Args : label perl v5.14.2 2012-03-02 Bio::LiveSeq::Range(3pm)
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Bio::LiveSeq::Gene(3pm) User Contributed Perl Documentation Bio::LiveSeq::Gene(3pm) NAME
Bio::LiveSeq::Gene - Range abstract class for LiveSeq SYNOPSIS
# documentation needed DESCRIPTION
This is used as storage for all object references concerning a particular gene. AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $gene = Bio::LiveSeq::Gene->new(-name => "name", -features => $hashref -upbound => $min -downbound => $max); Function: generates a new Bio::LiveSeq::Gene Returns : reference to a new object of class Gene Errorcode -1 Args : one string and one hashreference containing all features defined for the Gene and the references to the LiveSeq objects for those features. Two labels for defining boundaries of the gene. Usually the boundaries will reflect max span of transcript, exon... features, while the DNA sequence will be created with some flanking regions (e.g. with the EMBL_SRS::gene2liveseq routine). If these two labels are not given, they will default to the start and end of the DNA object. Note : the format of the hash has to be like DNA => reference to LiveSeq::DNA object Transcripts => reference to array of transcripts objrefs Transclations => reference to array of transcripts objrefs Exons => .... Introns => .... Prim_Transcripts => .... Repeat_Units => .... Repeat_Regions => .... Only DNA and Transcripts are mandatory verbose Title : verbose Usage : $self->verbose(0) Function: Sets verbose level for how ->warn behaves -1 = silent: no warning 0 = reduced: minimal warnings 1 = default: all warnings 2 = extended: all warnings + stack trace dump 3 = paranoid: a warning becomes a throw and the program dies Note: a quick way to set all LiveSeq objects at the same verbosity level is to change the DNA level object, since they all look to that one if their verbosity_level attribute is not set. But the method offers fine tuning possibility by changing the verbose level of each object in a different way. So for example, after $loader= and $gene= have been retrieved by a program, the command $gene->verbose(0); would set the default verbosity level to 0 for all objects. Returns : the current verbosity level Args : -1,0,1,2 or 3 perl v5.14.2 2012-03-02 Bio::LiveSeq::Gene(3pm)